Table 1

Functional evidence used.

Source

Number of gene sets

Number of significant motif modules


FDR = 0.05

FDR = 0.01


BioCarta

155

0

0


KEGG

168

122,279

10,378


Genmapp

88

5486

14


GO

1141

1,296,621

460,973


PicTar

162

2,645,699

1,647,433


Cancer Module

380

485,850

67,135


Total

2094

2,871,863

1,855,459


The first column lists the different sources of functional evidence. The second column is the number of all gene sets. The third and fourth columns are the number of motif modules whose target genes significantly overlap with the gene sets. All of them except KEGG pathways are downloaded from MSigDB. For KEGG pathways, we directly downloaded from the KEGG ftp site. Only the gene sets with at least ten genes are used.

Cai et al. BMC Genomics 2010 11:567   doi:10.1186/1471-2164-11-567

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